VMD plugin to calculate and visualize clusters of conformations for a trajectory
☆23Oct 24, 2018Updated 7 years ago
Alternatives and similar repositories for clustering
Users that are interested in clustering are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Convenience functions for VMD-TCL scripting☆14Jul 16, 2025Updated 8 months ago
- ☆11Oct 18, 2019Updated 6 years ago
- Fast PBC wrapping and unwrapping for VMD☆24Nov 25, 2024Updated last year
- ☆38Dec 6, 2012Updated 13 years ago
- Development version of the pbctools plugin for VMD.☆16Aug 19, 2025Updated 7 months ago
- Building and analyzing residue interaction networks with cofactors (includes tutorial).☆18Mar 31, 2021Updated 4 years ago
- Instructions for Building Software on Various Platforms☆17May 12, 2025Updated 10 months ago
- Workshop - Analysis of Molecular Dynamics Simulation Using Python☆19Aug 14, 2020Updated 5 years ago
- ☆14Dec 29, 2022Updated 3 years ago
- A Python package to compute and analyze transport properties.☆16Jul 27, 2025Updated 7 months ago
- Utilities for working with the RDKit☆20Sep 5, 2016Updated 9 years ago
- Using supervised machine learning to build collective variables for accelerated sampling☆28Jun 26, 2018Updated 7 years ago
- Enumerate conformational, protomeric, and pH-related microstates for docking with AutoDock☆44Mar 12, 2026Updated last week
- Learning Protein-Ligand Properties with Atomic Environment Vectors☆10Apr 19, 2024Updated last year
- Official repo of the Biomeccanica Multiscala course (prof. Marco A. Deriu) - Master Degree in Biomedical engineering, Politecnico di Tori…☆12Jan 2, 2025Updated last year
- Schrödinger 2D Sketcher☆24Updated this week
- PARCE version 1.0☆12Feb 1, 2021Updated 5 years ago
- Source code for "Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome inter…☆13Jun 17, 2022Updated 3 years ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆35Dec 10, 2025Updated 3 months ago
- COSMO: COarse-grained Simulation of intrinsically disordered prOteins with openMM☆15Feb 8, 2026Updated last month
- The Protein Feature View - a SVG library for visualising protein annotations☆13Sep 18, 2017Updated 8 years ago
- De novo drug design with deep interactome learning☆41Jun 12, 2025Updated 9 months ago
- Collection of scripts that integrates docking, virtual screening, similarity and molecular modeling programs.☆30Mar 4, 2026Updated 2 weeks ago
- Official code release for Ambient Protein Diffusion☆32Aug 30, 2025Updated 6 months ago
- Official repository for the Deep Docking protocol☆125Nov 30, 2023Updated 2 years ago
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆18Sep 11, 2022Updated 3 years ago
- iPBSA minimizes docked receptor-ligand conformations in implicit solvent and calculates the binding free energy with MM/PB(GB)SA methods.…☆13Oct 10, 2023Updated 2 years ago
- Adaptive sampling algorithms for molecular transitions☆25Updated this week
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Oct 21, 2020Updated 5 years ago
- WaterDock-2.0 implementation with Akshay Sridhar☆21Nov 2, 2023Updated 2 years ago
- ☆17Sep 14, 2022Updated 3 years ago
- ☆53Nov 24, 2022Updated 3 years ago
- Small molecules discovery with different active deep learning strategies. Codebase for the paper: "Traversing chemical space with active …☆28Aug 18, 2024Updated last year
- Robust and stable clustering of molecular dynamics simulation trajectories.☆19Sep 2, 2022Updated 3 years ago
- A Python package to calculate, visualize and analyze correlation maps of proteins.☆44Mar 14, 2026Updated last week
- ☆15Dec 4, 2023Updated 2 years ago
- MD pharmacophores and virtual screening☆34Dec 15, 2023Updated 2 years ago
- Generate customized voxel representations of protein-ligand complexes using GPU.☆11Sep 8, 2025Updated 6 months ago
- Implements the blood brain barrier score described in: J. Med. Chem. 2019, 62, 21, 9824-9836 (https://doi.org/10.1021/acs.jmedchem.9b0122…☆14Sep 27, 2020Updated 5 years ago